Add documentation for new CLI commands: docs-related-cli and lite-fix

- Implemented the `docs-related-cli` command for context-aware documentation generation and update for changed modules using CLI execution with tool fallback.
- Introduced the `lite-fix` command for lightweight bug diagnosis and fix workflow, featuring intelligent severity assessment and optional hotfix mode for production incidents.

.claude/skills/command-guide/reference/commands/workflow/tools/conflict-resolution.md

@@ -10,7 +10,7 @@ examples:
 # Conflict Resolution Command
 
 ## Purpose
-Analyzes conflicts between implementation plans and existing codebase, generating multiple resolution strategies.
+Analyzes conflicts between implementation plans and existing codebase, **including module scenario uniqueness detection**, generating multiple resolution strategies with **iterative clarification until boundaries are clear**.
 
 **Scope**: Detection and strategy generation only - NO code modification or task creation.
 
@@ -21,11 +21,14 @@ Analyzes conflicts between implementation plans and existing codebase, generatin
 | Responsibility | Description |
 |---------------|-------------|
 | **Detect Conflicts** | Analyze plan vs existing code inconsistencies |
+| **Scenario Uniqueness** | **NEW**: Search and compare new modules with existing modules for functional overlaps |
 | **Generate Strategies** | Provide 2-4 resolution options per conflict |
+| **Iterative Clarification** | **NEW**: Ask unlimited questions until scenario boundaries are clear and unique |
+| **Agent Re-analysis** | **NEW**: Dynamically update strategies based on user clarifications |
 | **CLI Analysis** | Use Gemini/Qwen (Claude fallback) |
-| **User Decision** | Present options, never auto-apply |
+| **User Decision** | Present options ONE BY ONE, never auto-apply |
 | **Direct Text Output** | Output questions via text directly, NEVER use bash echo/printf |
-| **Single Output** | `CONFLICT_RESOLUTION.md` with findings |
+| **Structured Data** | JSON output for programmatic processing, NO file generation |
 
 ## Conflict Categories
 
@@ -49,6 +52,13 @@ Analyzes conflicts between implementation plans and existing codebase, generatin
 - Setup conflicts
 - Breaking updates
 
+### 5. Module Scenario Overlap
+- **NEW**: Functional overlap between new and existing modules
+- Scenario boundary ambiguity
+- Duplicate responsibility detection
+- Module merge/split decisions
+- **Requires iterative clarification until uniqueness confirmed**
+
 ## Execution Flow
 
 ### Phase 1: Validation
@@ -76,20 +86,28 @@ Task(subagent_type="cli-execution-agent", prompt=`
   - Load plan from .workflow/active/{session_id}/.process/context-package.json
   - Extract role analyses and requirements
 
-  ### 2. Execute CLI Analysis
+  ### 2. Execute CLI Analysis (Enhanced with Scenario Uniqueness Detection)
 
   Primary (Gemini):
   cd {project_root} && gemini -p "
-  PURPOSE: Detect conflicts between plan and codebase
+  PURPOSE: Detect conflicts between plan and codebase, including module scenario overlaps
   TASK:
   • Compare architectures
   • Identify breaking API changes
   • Detect data model incompatibilities
   • Assess dependency conflicts
+  • **NEW: Analyze module scenario uniqueness**
+    - Extract new module functionality from plan
+    - Search all existing modules with similar functionality
+    - Compare scenario coverage and identify overlaps
+    - Generate clarification questions for boundary definition
   MODE: analysis
-  CONTEXT: @{existing_files} @.workflow/active/{session_id}/**/*
-  EXPECTED: Conflict list with severity ratings
-  RULES: Focus on breaking changes and migration needs
+  CONTEXT: @**/*.ts @**/*.js @**/*.tsx @**/*.jsx @.workflow/active/{session_id}/**/*
+  EXPECTED: Conflict list with severity ratings, including ModuleOverlap conflicts with:
+    - Existing module list with scenarios
+    - Overlap analysis matrix
+    - Targeted clarification questions
+  RULES: $(cat ~/.claude/workflows/cli-templates/prompts/analysis/02-analyze-code-patterns.txt) | Focus on breaking changes, migration needs, and functional overlaps | analysis=READ-ONLY
   "
 
   Fallback: Qwen (same prompt) → Claude (manual analysis)
@@ -98,9 +116,11 @@ Task(subagent_type="cli-execution-agent", prompt=`
 
   Template per conflict:
   - Severity: Critical/High/Medium
-  - Category: Architecture/API/Data/Dependency
+  - Category: Architecture/API/Data/Dependency/ModuleOverlap
   - Affected files + impact
+  - **For ModuleOverlap**: Include overlap_analysis with existing modules and scenarios
   - Options with pros/cons, effort, risk
+  - **For ModuleOverlap strategies**: Add clarification_needed questions for boundary definition
   - Recommended strategy + rationale
 
   ### 4. Return Structured Conflict Data
@@ -116,10 +136,10 @@ Task(subagent_type="cli-execution-agent", prompt=`
         "id": "CON-001",
         "brief": "一行中文冲突摘要",
         "severity": "Critical|High|Medium",
-        "category": "Architecture|API|Data|Dependency",
+        "category": "Architecture|API|Data|Dependency|ModuleOverlap",
         "affected_files": [
-          ".workflow/session/{session}/.brainstorm/guidance-specification.md",
-          ".workflow/session/{session}/.brainstorm/system-architect/analysis.md"
+          ".workflow/active/{session}/.brainstorm/guidance-specification.md",
+          ".workflow/active/{session}/.brainstorm/system-architect/analysis.md"
         ],
         "description": "详细描述冲突 - 什么不兼容",
         "impact": {
@@ -128,6 +148,23 @@ Task(subagent_type="cli-execution-agent", prompt=`
           "migration_required": true|false,
           "estimated_effort": "人天估计"
         },
+        "overlap_analysis": {
+          "// NOTE": "仅当 category=ModuleOverlap 时需要此字段",
+          "new_module": {
+            "name": "新模块名称",
+            "scenarios": ["场景1", "场景2", "场景3"],
+            "responsibilities": "职责描述"
+          },
+          "existing_modules": [
+            {
+              "file": "src/existing/module.ts",
+              "name": "现有模块名称",
+              "scenarios": ["场景A", "场景B"],
+              "overlap_scenarios": ["重叠场景1", "重叠场景2"],
+              "responsibilities": "现有模块职责"
+            }
+          ]
+        },
         "strategies": [
           {
             "name": "策略名称（中文）",
@@ -137,9 +174,15 @@ Task(subagent_type="cli-execution-agent", prompt=`
             "effort": "时间估计",
             "pros": ["优点1", "优点2"],
             "cons": ["缺点1", "缺点2"],
+            "clarification_needed": [
+              "// NOTE: 仅当需要用户进一步澄清时需要此字段（尤其是 ModuleOverlap）",
+              "新模块的核心职责边界是什么？",
+              "如何与现有模块 X 协作？",
+              "哪些场景应该由新模块处理？"
+            ],
             "modifications": [
               {
-                "file": ".workflow/session/{session}/.brainstorm/guidance-specification.md",
+                "file": ".workflow/active/{session}/.brainstorm/guidance-specification.md",
                 "section": "## 2. System Architect Decisions",
                 "change_type": "update",
                 "old_content": "原始内容片段（用于定位）",
@@ -147,7 +190,7 @@ Task(subagent_type="cli-execution-agent", prompt=`
                 "rationale": "为什么这样改"
               },
               {
-                "file": ".workflow/session/{session}/.brainstorm/system-architect/analysis.md",
+                "file": ".workflow/active/{session}/.brainstorm/system-architect/analysis.md",
                 "section": "## Design Decisions",
                 "change_type": "update",
                 "old_content": "原始内容片段",
@@ -204,155 +247,251 @@ Task(subagent_type="cli-execution-agent", prompt=`
 `)
 ```
 
-**Agent Internal Flow**:
+**Agent Internal Flow** (Enhanced):
 ```
 1. Load context package
 2. Check conflict_risk (exit if none/low)
 3. Read existing files + plan artifacts
-4. Run CLI analysis (Gemini→Qwen→Claude)
-5. Parse conflict findings
-6. Generate 2-4 strategies per conflict with modifications
+4. Run CLI analysis (Gemini→Qwen→Claude) with enhanced tasks:
+   - Standard conflict detection (Architecture/API/Data/Dependency)
+   - **NEW: Module scenario uniqueness detection**
+     * Extract new module functionality from plan
+     * Search all existing modules with similar keywords/functionality
+     * Compare scenario coverage and responsibilities
+     * Identify functional overlaps and boundary ambiguities
+     * Generate ModuleOverlap conflicts with overlap_analysis
+5. Parse conflict findings (including ModuleOverlap category)
+6. Generate 2-4 strategies per conflict:
+   - Include modifications for each strategy
+   - **For ModuleOverlap**: Add clarification_needed questions for boundary definition
 7. Return JSON to stdout (NOT file write)
 8. Return execution log path
 ```
 
-### Phase 3: User Confirmation via Text Interaction
+### Phase 3: Iterative User Interaction with Clarification Loop
 
-**Command parses agent JSON output and presents conflicts to user via text**:
+**Execution Flow**:
+```
+FOR each conflict (逐个处理，无数量限制):
+  clarified = false
+  round = 0
+  userClarifications = []
+
+  WHILE (!clarified && round < 10):
+    round++
+
+    // 1. Display conflict (包含所有关键字段)
+    - category, id, brief, severity, description
+    - IF ModuleOverlap: 展示 overlap_analysis
+      * new_module: {name, scenarios, responsibilities}
+      * existing_modules[]: {file, name, scenarios, overlap_scenarios, responsibilities}
+
+    // 2. Display strategies (2-4个策略 + 自定义选项)
+    - FOR each strategy: {name, approach, complexity, risk, effort, pros, cons}
+      * IF clarification_needed: 展示待澄清问题列表
+    - 自定义选项: {suggestions: modification_suggestions[]}
+
+    // 3. User selects strategy
+    userChoice = readInput()
+
+    IF userChoice == "自定义":
+      customConflicts.push({id, brief, category, suggestions, overlap_analysis})
+      clarified = true
+      BREAK
+
+    selectedStrategy = strategies[userChoice]
+
+    // 4. Clarification loop
+    IF selectedStrategy.clarification_needed.length > 0:
+      // 收集澄清答案
+      FOR each question:
+        answer = readInput()
+        userClarifications.push({question, answer})
+
+      // Agent 重新分析
+      reanalysisResult = Task(cli-execution-agent, prompt={
+        冲突信息: {id, brief, category, 策略}
+        用户澄清: userClarifications[]
+        场景分析: overlap_analysis (if ModuleOverlap)
+
+        输出: {
+          uniqueness_confirmed: bool,
+          rationale: string,
+          updated_strategy: {name, approach, complexity, risk, effort, modifications[]},
+          remaining_questions: [] (如果仍有歧义)
+        }
+      })
+
+      IF reanalysisResult.uniqueness_confirmed:
+        selectedStrategy = updated_strategy
+        selectedStrategy.clarifications = userClarifications
+        clarified = true
+      ELSE:
+        // 更新澄清问题，继续下一轮
+        selectedStrategy.clarification_needed = remaining_questions
+    ELSE:
+      clarified = true
+
+    resolvedConflicts.push({conflict, strategy: selectedStrategy})
+  END WHILE
+END FOR
+
+// Build output
+selectedStrategies = resolvedConflicts.map(r => ({
+  conflict_id, strategy, clarifications[]
+}))
+```
+
+**Key Data Structures**:
 
 ```javascript
-// 1. Parse agent JSON output
-const conflictData = JSON.parse(agentOutput);
-const conflicts = conflictData.conflicts; // No 4-conflict limit
-
-// 2. Format conflicts as text output (max 10 per round)
-const batchSize = 10;
-const batches = chunkArray(conflicts, batchSize);
-
-for (const [batchIdx, batch] of batches.entries()) {
-  const totalBatches = batches.length;
-
-  // Output batch header
-  console.log(`===== 冲突解决 (第 ${batchIdx + 1}/${totalBatches} 轮) =====\n`);
-
-  // Output each conflict in batch
-  batch.forEach((conflict, idx) => {
-    const questionNum = batchIdx * batchSize + idx + 1;
-    console.log(`【问题${questionNum} - ${conflict.category}】${conflict.id}: ${conflict.brief}`);
-
-    conflict.strategies.forEach((strategy, sIdx) => {
-      const optionLetter = String.fromCharCode(97 + sIdx); // a, b, c, ...
-      console.log(`${optionLetter}) ${strategy.name}`);
-      console.log(`   说明：${strategy.approach}`);
-      console.log(`   复杂度: ${strategy.complexity} | 风险: ${strategy.risk} | 工作量: ${strategy.effort}`);
-    });
-
-    // Add custom option
-    const customLetter = String.fromCharCode(97 + conflict.strategies.length);
-    console.log(`${customLetter}) 自定义修改`);
-    console.log(`   说明：根据修改建议自行处理，不应用预设策略`);
-
-    // Show modification suggestions
-    if (conflict.modification_suggestions && conflict.modification_suggestions.length > 0) {
-      console.log(`   修改建议：`);
-      conflict.modification_suggestions.forEach(suggestion => {
-        console.log(`   - ${suggestion}`);
-      });
-    }
-    console.log();
-  });
-
-  console.log(`请回答 (格式: 1a 2b 3c...)：`);
-
-  // Wait for user input
-  const userInput = await readUserInput();
-
-  // Parse answers
-  const answers = parseUserAnswers(userInput, batch);
+// Custom conflict tracking
+customConflicts[] = {
+  id, brief, category,
+  suggestions: modification_suggestions[],
+  overlap_analysis: { new_module{}, existing_modules[] }  // ModuleOverlap only
 }
 
-// 3. Build selected strategies (exclude custom selections)
-const selectedStrategies = answers.filter(a => !a.isCustom).map(a => a.strategy);
-const customConflicts = answers.filter(a => a.isCustom).map(a => ({
-  id: a.conflict.id,
-  brief: a.conflict.brief,
-  suggestions: a.conflict.modification_suggestions
-}));
+// Agent re-analysis prompt output
+{
+  uniqueness_confirmed: bool,
+  rationale: string,
+  updated_strategy: {
+    name, approach, complexity, risk, effort,
+    modifications: [{file, section, change_type, old_content, new_content, rationale}]
+  },
+  remaining_questions: string[]
+}
 ```
 
-**Text Output Example**:
+**Text Output Example** (展示关键字段):
+
 ```markdown
-===== 冲突解决 (第 1/1 轮) =====
+============================================================
+冲突 1/3 - 第 1 轮
+============================================================
+【ModuleOverlap】CON-001: 新增用户认证服务与现有模块功能重叠
+严重程度: High | 描述: 计划中的 UserAuthService 与现有 AuthManager 场景重叠
 
-【问题1 - Architecture】CON-001: 现有认证系统与计划不兼容
-a) 渐进式迁移
-   说明：保留现有系统，逐步迁移到新方案
-   复杂度: Medium | 风险: Low | 工作量: 3-5天
-b) 完全重写
-   说明：废弃旧系统，从零实现新认证
-   复杂度: High | 风险: Medium | 工作量: 7-10天
-c) 自定义修改
-   说明：根据修改建议自行处理，不应用预设策略
-   修改建议：
-   - 评估现有认证系统的兼容性，考虑是否可以通过适配器模式桥接
-   - 检查JWT token格式和验证逻辑是否需要调整
-   - 确保用户会话管理与新架构保持一致
+--- 场景重叠分析 ---
+新模块: UserAuthService | 场景: 登录, Token验证, 权限, MFA
+现有模块: AuthManager (src/auth/AuthManager.ts) | 重叠: 登录, Token验证
 
-【问题2 - Data】CON-002: 数据库 schema 冲突
-a) 添加迁移脚本
-   说明：创建数据库迁移脚本处理 schema 变更
-   复杂度: Low | 风险: Low | 工作量: 1-2天
-b) 自定义修改
-   说明：根据修改建议自行处理，不应用预设策略
-   修改建议：
-   - 检查现有表结构是否支持新增字段，避免破坏性变更
-   - 考虑使用数据库版本控制工具（如Flyway或Liquibase）
-   - 准备数据迁移和回滚策略
+--- 解决策略 ---
+1) 合并 (Low复杂度 | Low风险 | 2-3天)
+   ⚠️ 需澄清: AuthManager是否能承担MFA？
 
-请回答 (格式: 1a 2b)：
+2) 拆分边界 (Medium复杂度 | Medium风险 | 4-5天)
+   ⚠️ 需澄清: 基础/高级认证边界? Token验证归谁?
+
+3) 自定义修改
+   建议: 评估扩展性; 策略模式分离; 定义接口边界
+
+请选择 (1-3): > 2
+
+--- 澄清问答 (第1轮) ---
+Q: 基础/高级认证边界?
+A: 基础=密码登录+token验证, 高级=MFA+OAuth+SSO
+
+Q: Token验证归谁?
+A: 统一由 AuthManager 负责
+
+🔄 重新分析...
+✅ 唯一性已确认 | 理由: 边界清晰 - AuthManager(基础+token), UserAuthService(MFA+OAuth+SSO)
+
+============================================================
+冲突 2/3 - 第 1 轮 [下一个冲突]
+============================================================
 ```
 
-**User Input Examples**:
-- `1a 2a` → Conflict 1: 渐进式迁移, Conflict 2: 添加迁移脚本
-- `1b 2b` → Conflict 1: 完全重写, Conflict 2: 自定义修改
-- `1c 2c` → Both choose custom modification (user handles manually with suggestions)
+**Loop Characteristics**: 逐个处理 | 无限轮次(max 10) | 动态问题生成 | Agent重新分析判断唯一性 | ModuleOverlap场景边界澄清
 
 ### Phase 4: Apply Modifications
 
 ```javascript
-// 1. Extract modifications from selected strategies
+// 1. Extract modifications from resolved strategies
 const modifications = [];
-selectedStrategies.forEach(strategy => {
-  if (strategy !== "skip") {
-    modifications.push(...strategy.modifications);
+selectedStrategies.forEach(item => {
+  if (item.strategy && item.strategy.modifications) {
+    modifications.push(...item.strategy.modifications.map(mod => ({
+      ...mod,
+      conflict_id: item.conflict_id,
+      clarifications: item.clarifications
+    })));
   }
 });
 
+console.log(`\n正在应用 ${modifications.length} 个修改...`);
+
 // 2. Apply each modification using Edit tool
-modifications.forEach(mod => {
-  if (mod.change_type === "update") {
-    Edit({
-      file_path: mod.file,
-      old_string: mod.old_content,
-      new_string: mod.new_content
-    });
+const appliedModifications = [];
+const failedModifications = [];
+
+modifications.forEach((mod, idx) => {
+  try {
+    console.log(`[${idx + 1}/${modifications.length}] 修改 ${mod.file}...`);
+
+    if (mod.change_type === "update") {
+      Edit({
+        file_path: mod.file,
+        old_string: mod.old_content,
+        new_string: mod.new_content
+      });
+    } else if (mod.change_type === "add") {
+      // Handle addition - append or insert based on section
+      const fileContent = Read(mod.file);
+      const updated = insertContentAfterSection(fileContent, mod.section, mod.new_content);
+      Write(mod.file, updated);
+    } else if (mod.change_type === "remove") {
+      Edit({
+        file_path: mod.file,
+        old_string: mod.old_content,
+        new_string: ""
+      });
+    }
+
+    appliedModifications.push(mod);
+    console.log(`  ✓ 成功`);
+  } catch (error) {
+    console.log(`  ✗ 失败: ${error.message}`);
+    failedModifications.push({ ...mod, error: error.message });
   }
-  // Handle "add" and "remove" similarly
 });
 
-// 3. Update context-package.json
+// 3. Update context-package.json with resolution details
 const contextPackage = JSON.parse(Read(contextPath));
 contextPackage.conflict_detection.conflict_risk = "resolved";
-contextPackage.conflict_detection.resolved_conflicts = conflicts.map(c => c.id);
+contextPackage.conflict_detection.resolved_conflicts = selectedStrategies.map(s => ({
+  conflict_id: s.conflict_id,
+  strategy_name: s.strategy.name,
+  clarifications: s.clarifications
+}));
+contextPackage.conflict_detection.custom_conflicts = customConflicts.map(c => c.id);
 contextPackage.conflict_detection.resolved_at = new Date().toISOString();
 Write(contextPath, JSON.stringify(contextPackage, null, 2));
 
-// 4. Output custom conflict summary (if any)
+// 4. Output custom conflict summary with overlap analysis (if any)
 if (customConflicts.length > 0) {
-  console.log("\n===== 需要自定义处理的冲突 =====\n");
+  console.log(`\n${'='.repeat(60)}`);
+  console.log(`需要自定义处理的冲突 (${customConflicts.length})`);
+  console.log(`${'='.repeat(60)}\n`);
+
   customConflicts.forEach(conflict => {
-    console.log(`【${conflict.id}】${conflict.brief}`);
-    console.log("修改建议：");
+    console.log(`【${conflict.category}】${conflict.id}: ${conflict.brief}`);
+
+    // Show overlap analysis for ModuleOverlap conflicts
+    if (conflict.category === 'ModuleOverlap' && conflict.overlap_analysis) {
+      console.log(`\n场景重叠信息:`);
+      console.log(`  新模块: ${conflict.overlap_analysis.new_module.name}`);
+      console.log(`  场景: ${conflict.overlap_analysis.new_module.scenarios.join(', ')}`);
+      console.log(`\n  与以下模块重叠:`);
+      conflict.overlap_analysis.existing_modules.forEach(mod => {
+        console.log(`    - ${mod.name} (${mod.file})`);
+        console.log(`      重叠场景: ${mod.overlap_scenarios.join(', ')}`);
+      });
+    }
+
+    console.log(`\n修改建议:`);
     conflict.suggestions.forEach(suggestion => {
       console.log(`  - ${suggestion}`);
     });
@@ -360,24 +499,42 @@ if (customConflicts.length > 0) {
   });
 }
 
-// 5. Return summary
+// 5. Output failure summary (if any)
+if (failedModifications.length > 0) {
+  console.log(`\n⚠️ 部分修改失败 (${failedModifications.length}):`);
+  failedModifications.forEach(mod => {
+    console.log(`  - ${mod.file}: ${mod.error}`);
+  });
+}
+
+// 6. Return summary
 return {
-  resolved: modifications.length,
-  custom: customConflicts.length,
-  modified_files: [...new Set(modifications.map(m => m.file))],
-  custom_conflicts: customConflicts
+  total_conflicts: conflicts.length,
+  resolved_with_strategy: selectedStrategies.length,
+  custom_handling: customConflicts.length,
+  modifications_applied: appliedModifications.length,
+  modifications_failed: failedModifications.length,
+  modified_files: [...new Set(appliedModifications.map(m => m.file))],
+  custom_conflicts: customConflicts,
+  clarification_records: selectedStrategies.filter(s => s.clarifications.length > 0)
 };
 ```
 
 **Validation**:
 ```
-✓ Agent returns valid JSON structure
-✓ Text output displays all conflicts (max 10 per round)
-✓ User selections captured correctly
+✓ Agent returns valid JSON structure with ModuleOverlap conflicts
+✓ Conflicts processed ONE BY ONE (not in batches)
+✓ ModuleOverlap conflicts include overlap_analysis field
+✓ Strategies with clarification_needed display questions
+✓ User selections captured correctly per conflict
+✓ Clarification loop continues until uniqueness confirmed
+✓ Agent re-analysis returns uniqueness_confirmed and updated_strategy
+✓ Maximum 10 rounds per conflict safety limit enforced
 ✓ Edit tool successfully applies modifications
 ✓ guidance-specification.md updated
 ✓ Role analyses (*.md) updated
-✓ context-package.json marked as resolved
+✓ context-package.json marked as resolved with clarification records
+✓ Custom conflicts display overlap_analysis for manual handling
 ✓ Agent log saved to .workflow/active/{session_id}/.chat/
 ```
 
@@ -441,24 +598,38 @@ If Edit tool fails mid-application:
 - NO report file generation
 
 **User Interaction**:
-- Text-based strategy selection (max 10 conflicts per round)
+- **Iterative conflict processing**: One conflict at a time, not in batches
 - Each conflict: 2-4 strategy options + "自定义修改" option (with suggestions)
+- **Clarification loop**: Unlimited questions per conflict until uniqueness confirmed (max 10 rounds)
+- **ModuleOverlap conflicts**: Display overlap_analysis with existing modules
+- **Agent re-analysis**: Dynamic strategy updates based on user clarifications
 
 ### Success Criteria
 ```
-✓ CLI analysis returns valid JSON structure
-✓ Conflicts presented in batches (max 10 per round)
+✓ CLI analysis returns valid JSON structure with ModuleOverlap category
+✓ Agent performs scenario uniqueness detection (searches existing modules)
+✓ Conflicts processed ONE BY ONE with iterative clarification
 ✓ Min 2 strategies per conflict with modifications
+✓ ModuleOverlap conflicts include overlap_analysis with existing modules
+✓ Strategies requiring clarification include clarification_needed questions
 ✓ Each conflict includes 2-5 modification_suggestions
-✓ Text output displays all conflicts correctly with suggestions
-✓ User selections captured and processed
+✓ Text output displays conflict with overlap analysis (if ModuleOverlap)
+✓ User selections captured per conflict
+✓ Clarification loop continues until uniqueness confirmed (unlimited rounds, max 10)
+✓ Agent re-analysis with user clarifications updates strategy
+✓ Uniqueness confirmation based on clear scenario boundaries
 ✓ Edit tool applies modifications successfully
-✓ Custom conflicts displayed with suggestions for manual handling
+✓ Custom conflicts displayed with overlap_analysis for manual handling
 ✓ guidance-specification.md updated with resolved conflicts
 ✓ Role analyses (*.md) updated with resolved conflicts
-✓ context-package.json marked as "resolved"
+✓ context-package.json marked as "resolved" with clarification records
 ✓ No CONFLICT_RESOLUTION.md file generated
-✓ Modification summary includes custom conflict count
+✓ Modification summary includes:
+  - Total conflicts
+  - Resolved with strategy (count)
+  - Custom handling (count)
+  - Clarification records
+  - Overlap analysis for custom ModuleOverlap conflicts
 ✓ Agent log saved to .workflow/active/{session_id}/.chat/
 ✓ Error handling robust (validate/retry/degrade)
 ```

.claude/skills/command-guide/reference/commands/workflow/tools/context-gather.md

@@ -22,7 +22,7 @@ Orchestrator command that invokes `context-search-agent` to gather comprehensive
 - **Agent Delegation**: Delegate all discovery to `context-search-agent` for autonomous execution
 - **Detection-First**: Check for existing context-package before executing
 - **Plan Mode**: Full comprehensive analysis (vs lightweight brainstorm mode)
-- **Standardized Output**: Generate `.workflow/session/{session}/.process/context-package.json`
+- **Standardized Output**: Generate `.workflow/active/{session}/.process/context-package.json`
 
 ## Execution Flow
 
@@ -57,8 +57,6 @@ Task(
   subagent_type="context-search-agent",
   description="Gather comprehensive context for plan",
   prompt=`
-You are executing as context-search-agent (.claude/agents/context-search-agent.md).
-
 ## Execution Mode
 **PLAN MODE** (Comprehensive) - Full Phase 1-3 execution
 

.claude/skills/command-guide/reference/commands/workflow/tools/task-generate-agent.md

@@ -17,242 +17,140 @@ Autonomous task JSON and IMPL_PLAN.md generation using action-planning-agent wit
 - **Two-Phase Flow**: Discovery (context gathering) → Output (document generation)
 - **Memory-First**: Reuse loaded documents from conversation memory
 - **MCP-Enhanced**: Use MCP tools for advanced code analysis and research
-- **Pre-Selected Templates**: Command selects correct template based on `--cli-execute` flag **before** invoking agent
-- **Agent Simplicity**: Agent receives pre-selected template and focuses only on content generation
 - **Path Clarity**: All `focus_paths` prefer absolute paths (e.g., `D:\\project\\src\\module`), or clear relative paths from project root (e.g., `./src/module`)
 
 ## Execution Lifecycle
 
-### Phase 1: Discovery & Context Loading
-**⚡ Memory-First Rule**: Skip file loading if documents already in conversation memory
+### Phase 1: Context Preparation (Command Responsibility)
 
-**Agent Context Package**:
-```javascript
-{
-  "session_id": "WFS-[session-id]",
-  "execution_mode": "agent-mode" | "cli-execute-mode",  // Determined by flag
-  "task_json_template_path": "~/.claude/workflows/cli-templates/prompts/workflow/task-json-agent-mode.txt"
-                           | "~/.claude/workflows/cli-templates/prompts/workflow/task-json-cli-mode.txt",
-  // Path selected by command based on --cli-execute flag, agent reads it
-  "session_metadata": {
-    // If in memory: use cached content
-    // Else: Load from .workflow/active//{session-id}/workflow-session.json
-  },
-  "brainstorm_artifacts": {
-    // Loaded from context-package.json → brainstorm_artifacts section
-    "role_analyses": [
-      {
-        "role": "system-architect",
-        "files": [{"path": "...", "type": "primary|supplementary"}]
-      }
-    ],
-    "guidance_specification": {"path": "...", "exists": true},
-    "synthesis_output": {"path": "...", "exists": true},
-    "conflict_resolution": {"path": "...", "exists": true}  // if conflict_risk >= medium
-  },
-  "context_package_path": ".workflow/active//{session-id}/.process/context-package.json",
-  "context_package": {
-    // If in memory: use cached content
-    // Else: Load from .workflow/active//{session-id}/.process/context-package.json
-  },
-  "mcp_capabilities": {
-    "code_index": true,
-    "exa_code": true,
-    "exa_web": true
-  }
-}
+**Command prepares session paths and metadata, agent loads content autonomously.**
+
+**Session Path Structure**:
+```
+.workflow/active/WFS-{session-id}/
+├── workflow-session.json          # Session metadata
+├── .process/
+│   └── context-package.json       # Context package with artifact catalog
+├── .task/                         # Output: Task JSON files
+├── IMPL_PLAN.md                   # Output: Implementation plan
+└── TODO_LIST.md                   # Output: TODO list
 ```
 
-**Discovery Actions**:
-1. **Load Session Context** (if not in memory)
-   ```javascript
-   if (!memory.has("workflow-session.json")) {
-     Read(.workflow/active//{session-id}/workflow-session.json)
-   }
-   ```
+**Command Preparation**:
+1. **Assemble Session Paths** for agent prompt:
+   - `session_metadata_path`
+   - `context_package_path`
+   - Output directory paths
 
-2. **Load Context Package** (if not in memory)
-   ```javascript
-   if (!memory.has("context-package.json")) {
-     Read(.workflow/active//{session-id}/.process/context-package.json)
-   }
-   ```
+2. **Provide Metadata** (simple values):
+   - `session_id`
+   - `execution_mode` (agent-mode | cli-execute-mode)
+   - `mcp_capabilities` (available MCP tools)
 
-3. **Extract & Load Role Analyses** (from context-package.json)
-   ```javascript
-   // Extract role analysis paths from context package
-   const roleAnalysisPaths = contextPackage.brainstorm_artifacts.role_analyses
-     .flatMap(role => role.files.map(f => f.path));
-
-   // Load each role analysis file
-   roleAnalysisPaths.forEach(path => Read(path));
-   ```
-
-4. **Load Conflict Resolution** (from context-package.json, if exists)
-   ```javascript
-   if (contextPackage.brainstorm_artifacts.conflict_resolution?.exists) {
-     Read(contextPackage.brainstorm_artifacts.conflict_resolution.path)
-   }
-   ```
-
-5. **Code Analysis with Native Tools** (optional - enhance understanding)
-   ```bash
-   # Find relevant files for task context
-   find . -name "*auth*" -type f
-   rg "authentication|oauth" -g "*.ts"
-   ```
-
-6. **MCP External Research** (optional - gather best practices)
-   ```javascript
-   // Get external examples for implementation
-   mcp__exa__get_code_context_exa(
-     query="TypeScript JWT authentication best practices",
-     tokensNum="dynamic"
-   )
-   ```
+**Note**: Agent autonomously loads files based on context package content (dynamic, not fixed template). Brainstorming artifacts only loaded if they exist in session.
 
 ### Phase 2: Agent Execution (Document Generation)
 
-**Pre-Agent Template Selection** (Command decides path before invoking agent):
-```javascript
-// Command checks flag and selects template PATH (not content)
-const templatePath = hasCliExecuteFlag
-  ? "~/.claude/workflows/cli-templates/prompts/workflow/task-json-cli-mode.txt"
-  : "~/.claude/workflows/cli-templates/prompts/workflow/task-json-agent-mode.txt";
-```
-
 **Agent Invocation**:
 ```javascript
 Task(
   subagent_type="action-planning-agent",
   description="Generate task JSON and implementation plan",
   prompt=`
-## Execution Context
+## Task Objective
+Generate implementation plan (IMPL_PLAN.md), task JSONs, and TODO list for workflow session
 
-**Session ID**: WFS-{session-id}
-**Execution Mode**: {agent-mode | cli-execute-mode}
-**Task JSON Template Path**: {template_path}
+## MANDATORY FIRST STEPS
+1. Read session metadata: {session.session_metadata_path}
+2. Load context package: {session.context_package_path}
+3. **Dynamically load files based on context package content** (see below)
 
-## Phase 1: Discovery Results (Provided Context)
+## Dynamic Content Loading Strategy
 
-### Session Metadata
-{session_metadata_content}
+**Load files based on what exists in context package - NOT a fixed template**
 
-### Role Analyses (Enhanced by Synthesis)
-{role_analyses_content}
-- Includes requirements, design specs, enhancements, and clarifications from synthesis phase
+### Step 1: Always Load (Required)
+- **Session Metadata** → Extract user input
+  - User description: Original task requirements
+  - Project scope and boundaries
+  - Technical constraints
 
-### Artifacts Inventory
-- **Guidance Specification**: {guidance_spec_path}
-- **Role Analyses**: {role_analyses_list}
+### Step 2: Check Context Package (Conditional Loading)
 
-### Context Package
-{context_package_summary}
-- Includes conflict_risk assessment
+**If `brainstorm_artifacts` exists in context package:**
+- Load artifacts **in priority order** as listed below
+- **If `brainstorm_artifacts` does NOT exist**: Skip to Step 3
 
-### Conflict Resolution (Conditional)
-If conflict_risk was medium/high, modifications have been applied to:
-- **guidance-specification.md**: Design decisions updated to resolve conflicts
-- **Role analyses (*.md)**: Recommendations adjusted for compatibility
-- **context-package.json**: Marked as "resolved" with conflict IDs
-- NO separate CONFLICT_RESOLUTION.md file (conflicts resolved in-place)
+**Priority Loading (when artifacts exist):**
+1. **guidance-specification.md** (if `guidance_specification.exists = true`)
+   - Overall design framework - use as primary reference
 
-### MCP Analysis Results (Optional)
-**Code Structure**: {mcp_code_index_results}
-**External Research**: {mcp_exa_research_results}
+2. **Role Analyses** (if `role_analyses[]` array exists)
+   - Load ALL role analysis files listed in array
+   - Each file path: `role_analyses[i].files[j].path`
 
-## Phase 2: Document Generation Task
+3. **Synthesis Output** (if `synthesis_output.exists = true`)
+   - Integrated view with clarifications
 
-**Agent Configuration Reference**: All task generation rules, quantification requirements, quality standards, and execution details are defined in action-planning-agent.
+4. **Conflict Resolution** (if `conflict_risk` = "medium" or "high")
+   - Check `conflict_resolution.status`
+   - If "resolved": Use updated artifacts (conflicts pre-addressed)
 
-Refer to: @.claude/agents/action-planning-agent.md for:
-- Task Decomposition Standards
-- Quantification Requirements (MANDATORY)
-- 5-Field Task JSON Schema
-- IMPL_PLAN.md Structure
-- TODO_LIST.md Format
-- Execution Flow & Quality Validation
+### Step 3: Extract Project Context
+- `focus_areas`: Target directories for implementation
+- `assets`: Existing code patterns to reuse
 
-### Required Outputs Summary
+## Session Paths
+- Session Metadata: .workflow/active/{session-id}/workflow-session.json
+- Context Package: .workflow/active/{session-id}/.process/context-package.json
+- Output Task Dir: .workflow/active/{session-id}/.task/
+- Output IMPL_PLAN: .workflow/active/{session-id}/IMPL_PLAN.md
+- Output TODO_LIST: .workflow/active/{session-id}/TODO_LIST.md
 
-#### 1. Task JSON Files (.task/IMPL-*.json)
-- **Location**: `.workflow/active//{session-id}/.task/`
-- **Template**: Read from `{template_path}` (pre-selected by command based on `--cli-execute` flag)
-- **Schema**: 5-field structure (id, title, status, meta, context, flow_control) with artifacts integration
-- **Details**: See action-planning-agent.md § Task JSON Generation
+## Context Metadata
+- Session ID: {session-id}
+- Execution Mode: {agent-mode | cli-execute-mode}
+- MCP Capabilities Available: {exa_code, exa_web, code_index}
 
-#### 2. IMPL_PLAN.md
-- **Location**: `.workflow/active//{session-id}/IMPL_PLAN.md`
-- **Template**: `~/.claude/workflows/cli-templates/prompts/workflow/impl-plan-template.txt`
-- **Details**: See action-planning-agent.md § Implementation Plan Creation
+**Note**: Content loading is **dynamic** based on actual files in session, not a fixed template
 
-#### 3. TODO_LIST.md
-- **Location**: `.workflow/active//{session-id}/TODO_LIST.md`
-- **Format**: Hierarchical task list with status indicators (▸, [ ], [x]) and JSON links
-- **Details**: See action-planning-agent.md § TODO List Generation
+## Expected Deliverables
+1. **Task JSON Files** (.task/IMPL-*.json)
+   - 6-field schema (id, title, status, context_package_path, meta, context, flow_control)
+   - Quantified requirements with explicit counts
+   - Artifacts integration from context package
+   - Flow control with pre_analysis steps
 
-### Agent Execution Summary
+2. **Implementation Plan** (IMPL_PLAN.md)
+   - Context analysis and artifact references
+   - Task breakdown and execution strategy
+   - Complete structure per agent definition
 
-**Key Steps** (Detailed instructions in action-planning-agent.md):
-1. Load task JSON template from provided path
-2. Extract and decompose tasks with quantification
-3. Generate task JSON files enforcing quantification requirements
-4. Create IMPL_PLAN.md using template
-5. Generate TODO_LIST.md matching task JSONs
-6. Update session state
+3. **TODO List** (TODO_LIST.md)
+   - Hierarchical structure with status indicators (▸, [ ], [x])
+   - Links to task JSONs and summaries
+   - Matches task JSON hierarchy
 
-**Quality Gates** (Full checklist in action-planning-agent.md):
-- ✓ Quantification requirements enforced (explicit counts, measurable acceptance, exact targets)
-- ✓ Task count ≤10 (hard limit)
-- ✓ Artifact references mapped correctly
-- ✓ MCP tool integration added
-- ✓ Documents follow template structure
+## Quality Standards
+- Task count ≤12 (hard limit)
+- All requirements quantified (explicit counts and lists)
+- Acceptance criteria measurable (verification commands)
+- Artifact references mapped from context package
+- All documents follow agent-defined structure
 
-## Output
-
-Generate all three documents and report completion status:
-- Task JSON files created: N files
-- Artifacts integrated: synthesis-spec, guidance-specification, N role analyses
-- MCP enhancements: code-index, exa-research
-- Session ready for execution: /workflow:execute
+## Success Criteria
+- All task JSONs valid and saved to .task/ directory
+- IMPL_PLAN.md created with complete structure
+- TODO_LIST.md generated matching task JSONs
+- Return completion status with file count
 `
 )
 ```
 
-
-### Agent Context Passing
-
-**Memory-Aware Context Assembly**:
-```javascript
-// Assemble context package for agent
-const agentContext = {
-  session_id: "WFS-[id]",
-
-  // Use memory if available, else load
-  session_metadata: memory.has("workflow-session.json")
-    ? memory.get("workflow-session.json")
-    : Read(.workflow/active/WFS-[id]/workflow-session.json),
-
-  context_package_path: ".workflow/active/WFS-[id]/.process/context-package.json",
-
-  context_package: memory.has("context-package.json")
-    ? memory.get("context-package.json")
-    : Read(".workflow/active/WFS-[id]/.process/context-package.json"),
-
-  // Extract brainstorm artifacts from context package
-  brainstorm_artifacts: extractBrainstormArtifacts(context_package),
-
-  // Load role analyses using paths from context package
-  role_analyses: brainstorm_artifacts.role_analyses
-    .flatMap(role => role.files)
-    .map(file => Read(file.path)),
-
-  // Load conflict resolution if exists (from context package)
-  conflict_resolution: brainstorm_artifacts.conflict_resolution?.exists
-    ? Read(brainstorm_artifacts.conflict_resolution.path)
-    : null,
-
-  // Optional MCP enhancements
-  mcp_analysis: executeMcpDiscovery()
-}
-```
+**Key Changes from Previous Version**:
+1. **Paths over Content**: Provide file paths for agent to read, not embedded content
+2. **MANDATORY FIRST STEPS**: Explicit requirement to load session metadata and context package
+3. **Complete Session Paths**: All file paths provided for agent operations
+4. **Emphasized Deliverables**: Clear deliverable requirements with quality standards
+5. **No Agent Self-Reference**: Removed "Refer to action-planning-agent.md" (agent knows its own definition)
+6. **No Template Paths**: Removed all template references (agent has complete schema/structure definitions)

.claude/skills/command-guide/reference/commands/workflow/tools/task-generate-tdd.md

@@ -30,11 +30,6 @@ Autonomous TDD task JSON and IMPL_PLAN.md generation using action-planning-agent
 - **1 feature = 1 task** containing complete TDD cycle internally
 - Each task executes Red-Green-Refactor phases sequentially
 - Task count = Feature count (typically 5 features = 5 tasks)
-- **Benefits**:
-  - 70% reduction in task management overhead
-  - Continuous context per feature (no switching between TEST/IMPL/REFACTOR)
-  - Simpler dependency management
-  - Maintains TDD rigor through internal phase structure
 
 **Previous Approach** (Deprecated):
 - 1 feature = 3 separate tasks (TEST-N.M, IMPL-N.M, REFACTOR-N.M)
@@ -499,11 +494,7 @@ IMPL (Green phase) tasks include automatic test-fix cycle:
    - **Repeat**: Up to max_iterations (default: 3)
 5. **Safety Net**: Auto-revert all changes if max iterations reached
 
-**Key Benefits**:
-- Faster feedback loop within Green phase
-- Autonomous recovery from initial implementation errors
-- Systematic debugging with Gemini's bug-fix template
-- Safe rollback prevents broken TDD state
+
 
 ## Configuration Options
 - **meta.max_iterations**: Number of fix attempts (default: 3 for TDD, 5 for test-gen)